Encephalomyocarditis virus (EMCV) infection causes viral encephalitis; however, the mechanisms underlying blood-brain barrier (BBB) disruption remain poorly understood. Here, we demonstrate that EMCV actively replicates in mouse brain tissue, induces robust neuroinflammation characterized by elevated proinflammatory cytokines and chemokines, and markedly increases BBB permeability as evidenced by Evans blue and sodium fluorescein extravasation. Importantly, tight junction (TJ) proteins ZO-1 and Occludin are selectively degraded at the post-transcriptional level, whereas Claudin-5 expression remains stable. Consistently, in vitro BBB models confirmed EMCV traversal, reduced transendothelial electrical resistance, and TJ disruption. Mechanistically, EMCV induces biphasic PI3K/AKT modulation and specifically downregulates AKT3. Notably, AKT3 knockdown exacerbates both autophagy and apoptosis, thereby accelerating ZO-1 and Occludin degradation while promoting viral replication. Furthermore, pharmacological inhibition of autophagy (chloroquine) or apoptosis (Z-VAD-FMK) effectively rescues TJ proteins and reduces viral load. Interestingly, the Caspase-8 inhibitor Z-IETD-FMK provides the most robust protection, implicating the extrinsic apoptotic pathway as the dominant route. Collectively, EMCV sequentially activates non-redundant AKT3-dependent autophagic and apoptotic pathways to degrade TJ proteins, ultimately enabling viral traversal across the compromised BBB and offering therapeutic targets for viral encephalitis.